consistent spelling of colour and other things in the docs.

In documentation under Colour Schemes
ClustalX doc uses color all the rest use colour.
The clustalX doc is also centred, while the others are not. The text looks like it was lifted from a paper/someone else's docs. We should show the reference to clustalX.

The following is just a documentation lag...

On the explanation of UPGMA, it says that plans are afoot to read in trees, but it can do this now, can't it?

Under PCA. Does the SeqSpace server at EBI still exist? If so, it may be an idea to provide a link.